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CGD / Cucurbit Genomics Database

A database which offers gene annotation of cucurbit. This base offers the genome of Melon (Cucumis melo), Cucumber (Cucumis sativus), Watermelon (Citrullus lanatus), Pumpkin (Cucurbita maxima). The Cucurbitaceae consist of 98 proposed genera with 975 species, mainly in regions tropical and subtropical. All species are sensitive to frost. Most of the plants in this family are annual vines, but some are woody lianas, thorny shrubs, or trees (Dendrosicyos). Cucurbit belongs to the Cucurbitaceae family.

KAIKOcDNA

Provides a repository for silkworm genome information for functional and applied genomics, including data from KAIKO2DDB of proteome data, Bombyx trap database for transgene and reporter data. KAIKOcDNA compiles genomic sequences, map information and expressed sequence tags (EST) data. The database makes available 4 map viewers: gene viewer, sequence search, keyword and position search systems. Results can be visualized at the level of nucleotide sequence, gene, scaffold and chromosome.

BDGP / Berkeley Drosophila Genome Project

Provides sequence of euchromatic genome of Drosophila melanogaster in high quality. BDGP is a resource developed to (i) produce gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans, (ii) characterize sequence and expression of cDNAs and (iii) develop informatics tools that support the experimental process, identify features of DNA sequence, and allow to present up-to-date information about annotated sequence to the research community.

tomatEST / Tomato Expressed Sequence Tag

Supports investigations on expressed sequence data from multiple tomato species. tomatEST is a database of expressed sequence tag (EST) /complementary DNA (cDNA) sequences from dbEST libraries, a division of GenBank containing sequence data. This resource was developed to provide a workbench for mining the complexity of EST sequence information content from multiple tomato species (i) for expression pattern analysis and (ii) for gene discovery in the framework of Solanum lycopersicum genome project.

FLAGdb++

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.

CR-EST / CRop EST database

Provides access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200,000 sequences derived from 48 cDNA libraries of six species: barley, wheat, pea, petunia, tobacco and potato. The barley section comprises approximately one-third of all publicly available ESTs. CR-EST deploys an automatic EST preparation pipeline that includes the identification of chimeric clones in order to transparently display the data quality. Sequences are clustered in species-specific projects to currently generate a non-redundant set of approximately 45,000 consensus sequences.

Pleurochrysome

Stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, Pleurochrysome also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes.

ocsESTdb

Collects oil crop seed ESTs and unigenes from B. napus, G. max, S. indicum and A. hypogaea and supplies a public resource for researchers to comparatively analyse and investigate oil accumulation metabolism. ocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.

SABRE2 / Systematic consolidation of Arabidopsis and other Botanical Resources

Cross-searches plant genetic resources through publicly available Arabidopsis information. In SABRE, plant expressed sequence tag (EST)/cDNA clones are related to TAIR (The Arabidoposis Information Resource) gene models and their annotations through sequence similarity. By entering a keyword, SABRE searches and retrieves TAIR gene models and annotations, together with homologous gene clones from various plant species. SABRE thus facilitates using TAIR annotations of Arabidopsis genes for research on homologous genes from other model plants.

LSD / Littorina sequence database

Facilitates genome research in Littorina saxatilis and related species. LSD was built by operating a hybrid assembly between four different expressed sequence tag (EST) data sets: two based on Sanger sequencing and two based on 454 sequencing. It can be useful to find markers such as microsatellites, single nucleotide polymorphisms (SNPs) useful for studies of population structure and phylogeny, and for genetic mapping and population genomic approaches.

WikiCell

Provides a unified view of the human transcriptome. WikiCell is an open and public platform dedicated to the annotation of the human transcriptome. Researchers can contribute transcriptome data, including ESTs and annotations. The wiki format allows authors to create and edit any number of interlinked webpages. Based on the anatomy of the human body, the logical structure traces out an image of refined classification from nine major systems to cell level, and includes both physiological and pathological transcriptome data. WikiCell can be searched by organ, tissue, and cell type, as well as GenBank accession number.

ANEXdb

Handles both microarray expression data and sequence assembly and annotation data. ANEXdb is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. Although ANEXdb currently houses porcine-specific data, it has been designed to be species independent. ANEXdb can be easily customized for other species by populating the databases with the relevant annotation and expression data from a variety of platforms such as Affymetrix GeneChips in other species or custom arrays.

PIP / Potential Intron Polymorphism

New
Provides access to information about potential intron polymorphism (PIP) markers and homologous relationships among PIP markers from different plant species. PIP contains more than 55,000 PIP markers for about 60 plant species. Users can search the database by (i) species name, (ii) marker ID, (iii) gene name in subject species, (iv) PlantGDB PUT ID, (v) intron length range in subject species, (vi) Gene Ontology (GO) number in subject species and (vii) gene description in subject species.

XDB3 / Xenopus Developmental Biology database

Gathers information about NIBB/NIG/NBRP Xenopus laevis expressed sequence tags (EST). XDB3 is composed of more than 250,000 EST information such as EST sequences, assembled contig sequences and their simple annotation. The database aims to help in designing polymerase chain reaction (PCR) primers and Morpholino oligos to clone genes, viewing the spatial expression patterns from unfertilized egg to tadpole stage, or knocking out genes of interest.

Morning Glory

Provides a database of Japanese morning glory. Morning Glory is an online resource of Ipomoea nil or Pharbitis nil, a floricultural plant of Japan. This project collects, develops and distributes mutant strains, expressed sequence tag (EST) clones, linkage maps, and transgenic lines of the Japanese morning glory to both local and foreign biologists. These resources can contribute to genome and genetic analysis, and development of new cultivars in the Japanese morning glory and related species.